Locus 2782

Sequence ID	X_DroMel_CAF1
Location	7,470,645 – 7,470,932
Length	287
Max. P	0.985092

overview

Window 6

Location	7,470,645 – 7,470,738
Length	93
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.38
Mean single sequence MFE	-22.09
Consensus MFE	-18.97
Energy contribution	-19.37
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.31
Structure conservation index	0.86
SVM decision value	2.00
SVM RNA-class probability	0.985092
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7470645 93 + 22224390
CUUUUCACUUCCU------------------CCCCCUG--GUCCUCGUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUC
.............------------------.......--((((((((((((-------................((((....)))).))))))).)))))((..(((.....)))..)) ( -21.03)
>DroSec_CAF1 3904 93 + 1
CUCUUCACUUCCU------------------CCCCGUG--GUCCUCGUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUC
.............------------------....((.--((((((((((((-------................((((....)))).))))))).))))).))((((.....))))... ( -23.53)
>DroSim_CAF1 5617 93 + 1
CUUUUCACUUCCU------------------CCCCGUG--GUCCUCGUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUC
.............------------------....((.--((((((((((((-------................((((....)))).))))))).))))).))((((.....))))... ( -23.53)
>DroEre_CAF1 4245 97 + 1
CUUUUCACUACC--------------CCUCCCCCCAUG--GUCCUCCUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUC
........((((--------------(..........(--(....))....(-------(.((((((......(((((((.....)))))))..)))))).))..........))))).. ( -19.10)
>DroYak_CAF1 6328 120 + 1
CUUUUCACUUCCUCAUCUGCCCCCCCCCCCCCCCUUUGGUGUCCUCCUACUUCUCCCUUCUUCUUUCCCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUC
............................(((......((((((.((((.........................(((((((.....)))))))....)))).))))))......))).... ( -23.25)
>consensus
CUUUUCACUUCCU__________________CCCCGUG__GUCCUCGUACUU_______CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUC
........................................((((((((((((.......................((((....)))).))))))).)))))((..(((.....)))..)) (-18.97 = -19.37 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	7,470,665 – 7,470,774
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.21
Mean single sequence MFE	-24.57
Consensus MFE	-23.03
Energy contribution	-23.43
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.14
Structure conservation index	0.94
SVM decision value	0.31
SVM RNA-class probability	0.681917
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7470665 109 + 22224390
GUCCUCGUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUCCUCUUUUCUCUUCUCCGGCUGUCCAUGUCCGUUCCG----
((((((((((((-------................((((....)))).))))))).)))))((((...(((.(((..(.((...............)).)..)))))).))))...---- ( -25.09)
>DroSec_CAF1 3924 109 + 1
GUCCUCGUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUCCUCUUUUCUCUUCUCCGGCUGUCCAUGUCCGUUCCG----
((((((((((((-------................((((....)))).))))))).)))))((((...(((.(((..(.((...............)).)..)))))).))))...---- ( -25.09)
>DroSim_CAF1 5637 109 + 1
GUCCUCGUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUCCUCUUUUCUCUUCUCCGGCUGUCCAUGUCCGUUCAG----
((((((((((((-------................((((....)))).))))))).)))))((((...(((.(((..(.((...............)).)..)))))).))))...---- ( -25.09)
>DroEre_CAF1 4269 109 + 1
GUCCUCCUACUU-------CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUCCUCCUCACUCUUCUCCGGCUGUCCAUGUCCGUUCCG----
............-------..............(((((((.....)))))))..(((((((((((((.(....((((.........))))....).))).)))...)))).)))..---- ( -22.80)
>DroYak_CAF1 6368 120 + 1
GUCCUCCUACUUCUCCCUUCUUCUUUCCCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUCCUCUUUUCUCUGCUCCGGCUGUCCAUGUCCGUUCUGUUCC
.................................(((((((.....)))))))..(((((((((((((.(((..(((.........)))..)))...))).)))...)))).)))...... ( -24.80)
>consensus
GUCCUCGUACUU_______CUUCUUUCUCCACAACUCGUUAUUACGACGAGUACGAAGGACGACGCCUGCACUGGGUAUCCUCUUUUCUCUUCUCCGGCUGUCCAUGUCCGUUCCG____
((((((((((((.......................((((....)))).))))))).)))))((((...(((.(((..(.((...............)).)..)))))).))))....... (-23.03 = -23.43 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	7,470,774 – 7,470,869
Length	95
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	87.60
Mean single sequence MFE	-31.62
Consensus MFE	-22.14
Energy contribution	-21.89
Covariance contribution	-0.25
Combinations/Pair	1.14
Mean z-score	-2.60
Structure conservation index	0.70
SVM decision value	0.99
SVM RNA-class probability	0.895931
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7470774 95 - 22224390
GUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCCC---UAUGUAUGGGGUAGGGUCUUUC------GGAGAGUCAGUGUCGACGCACUCAAAACUGAA
(((((((....(((......)))(((((((...((((((((---(((.......))))))))))).------.)))))))....)))))))............. ( -33.60)
>DroSec_CAF1 4033 95 - 1
GUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCCC---UAUAUAUGGGGUAGGGUCUUUC------GGGGAGUCAGUGUCGACGCACUCAGAACUGAA
(((((((....(((......)))(((((((...((((((((---(((.......))))))))))).------.)))))))....)))))))..(((....))). ( -33.50)
>DroSim_CAF1 5746 95 - 1
GUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCCC---UAUAUAUGGGGUAGGGUCUUUC------GGGGAGUCAGUGUCGACGCACUCAGAACUGAA
(((((((....(((......)))(((((((...((((((((---(((.......))))))))))).------.)))))))....)))))))..(((....))). ( -33.50)
>DroEre_CAF1 4378 99 - 1
GUGUUGAAGGACCAAAAGGAUGGGAGUUUUAUAGGGGGC-UUCU---CU-AUGGGUAGGGUCUUCAGUGGGGGGGGAGUCAGUGUCGACGCACUCAGAACUGAA
........(((((........(((((((((....)))))-))))---((-(....))))))))(((((...(((...(((......)))...)))...))))). ( -25.90)
>consensus
GUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCCC___UAUAUAUGGGGUAGGGUCUUUC______GGGGAGUCAGUGUCGACGCACUCAGAACUGAA
(((((((....(((......)))(((((((...((((((((................))))))))........)))))))....)))))))..(((....))). (-22.14 = -21.89 +  -0.25)

alignment

secondary structure

dotplot

Window 9

Location	7,470,829 – 7,470,932
Length	103
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	86.45
Mean single sequence MFE	-29.65
Consensus MFE	-21.67
Energy contribution	-21.80
Covariance contribution	0.13
Combinations/Pair	1.08
Mean z-score	-1.54
Structure conservation index	0.73
SVM decision value	0.14
SVM RNA-class probability	0.604710
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7470829 103 - 22224390
UGCAGAGGCAUGCCCGCAAGGUCUUUGGAAGGA-------------AGGAGGGAUUCCGAUUGUGAGGAGAAGGGUGUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCC
.((...(((((((((......((((.....(((-------------(.......))))......))))....)))))))))((((..(((......)))..))))........)). ( -26.80)
>DroSec_CAF1 4088 103 - 1
UGCAGAGGCAUGCCCGCAAGGUCUUUAGAAGGC-------------AGGAGGGAUUCCGAUUGUGAGGAGAAGGGUGUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCC
.((...(((((((((......((((((.((...-------------.((((...))))..)).))))))...)))))))))((((..(((......)))..))))........)). ( -27.90)
>DroSim_CAF1 5801 103 - 1
UGCAGAGGCAUGCCCGCAAGGUCUUUAGAAGGC-------------AGGAGGGAUUCCGAUUGUGAGGAGAAGGGUGUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCC
.((...(((((((((......((((((.((...-------------.((((...))))..)).))))))...)))))))))((((..(((......)))..))))........)). ( -27.90)
>DroYak_CAF1 6562 116 - 1
UGCAGAGGCAUACCCGCAAGGUCCUUGGAAGGAAGAAGGGAUCGGAAGGAGGGAUUCCGAUUGCUAGGAGAUGGGUGUGUUGAAGGACCAAACGGAUGGGAGCUUCAAAAGGGGGG
......(((((((((((....((((....))))...((.((((((((.......)))))))).))....).))))))))))((((..(((......)))...)))).......... ( -36.00)
>consensus
UGCAGAGGCAUGCCCGCAAGGUCUUUAGAAGGA_____________AGGAGGGAUUCCGAUUGUGAGGAGAAGGGUGUGUUGAAGGACCAAAAGGAUGGGACUUUUAUAGGAGGCC
......(((((((((.....((((((.......................))))))(((........)))...)))))))))((((..(((......)))..))))........... (-21.67 = -21.80 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:09 2006